Hit escape to bring up your menu, go to Interface, then Addons, then PetBattle Team. Toward the bottom there is a button labeled "Reconstruct Teams". Try clicking on that and see if it doesn't rebuild the previous teams (or most of them) that you had.

It's also worth noting that if you still have problems, you can try the Rematch Addon which has an import button in the options menu to import all your PBT saved teams (it makes copies so it doesn't affect PBT at all). Sometimes this works in at least generating the teams in Rematch so you have something to work from instead of just scratch.